I did the opposite actually, I up-sampled the DWIs so they are in the
same space as the T2w (using flirt with dof=6). I figured the unwarping
would be more accurate at a higher resolution. I also wanted to do all
my DTI and tractography analysis in this space anyway so It was a
convenient thing for me to do.
Mark
On 22/03/2013 18:05, Andreas Bartsch wrote:
> Hi Mark,
>
> thanks. It does look reassuring. I will try it myself, I quite like the
> idea.
> One question: Your T2 was of the same dimensions like your B0 image ord
> did you downsample it to the B0 resolution? Often, the T2 will be of a
> higher res than the B0, at least when it come to in plane resolution.
> Cheers,
> Andreas
>
> Am 22.03.13 17:02 schrieb "Mark Drakesmith" unter
> <[log in to unmask]>:
>
>> Hi Andreas
>>
>> I've attached images of the T2w, distorted and corrected B0 images.
>>
>> The topup call was:
>>
>> topup --imain=T2w_images_topup.nii.gz --datain=topup_dti_params.txt
>> --config=b02b0.cnf --out=my_topup_results --fout=my_field
>> --iout=my_unwarped_images -v
>>
>> The T2w_images_topup.nii.gz image contained the original B0 and the T2w
>> images. Note that the B0 image was rigidly transformed with flirt so it
>> is in the same voxel space a the T2w. the topup_dti_params.txt file
>> contained the following lines, corresponding to the B0 and T2w images
>> respectively. As per Jespers, suggestion the readout time for the T2w
>> was set close to zero:
>>
>> 0 1 0 0.0864
>> 0 1 0 0.00000001
>>
>> I've not yet applied this the full set of DWIs yet, but so far it looks
>> good.
>>
>> I hope this is of help.
>>
>> Mark
>>
>>
>> Dr. Mark Drakesmith
>> Research Associate
>>
>> Caridff University Brain Research Imaging Centre (CUBRIC)
>> School of Psychology
>> Cardiff University
>> Park Place
>> Cardiff
>> CF10 3AT
>>
>> Tel: +44 (0) 29 2087 0354
>> Fax: +44 (0) 29 2087 0339
>>
>> On 22/03/13 15:34, Andreas Bartsch wrote:
>>> Hi Mark,
>>>
>>> I have followed this with interest.
>>> Could you post an example (e.g. a slicer output) along with your topup
>>> call?
>>> You can also email me directly.
>>> Cheers,
>>> Andreas
>>>
>>> Am 22.03.13 15:53 schrieb "Mark Drakesmith" unter
>>> <[log in to unmask]>:
>>>
>>>> Hi Jesper
>>>>
>>>> I just tried it. It works beautifully! I didn't realise you could use
>>>> topup in that way (I had just followed the example in the FSL wiki).
>>>>
>>>> Thanks very much! :)
>>>>
>>>> Mark
>
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